8EKT | pdb_00008ekt

CYP51 from Acanthamoeba castellanii in complex with the tetrazole-based IND inhibitor VT-1161(VT1)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	298	18% PEG8000, 0.1 M sodium citrate, 0.34 mM n-dodecyl-b-D-maltoside 5.5 mM TCEP

Crystal Properties
Matthews coefficient	Solvent content
3.04	59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.453	α = 81.22
b = 99.304	β = 84.08
c = 107.915	γ = 60.08

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX-300	Be lens	2022-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.28	30	98.3	0.04	0.993	25	3.9		118963			32.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.28	2.32			1.02	0.539	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 7UWP	2.29	29.89	118963	6472	79	0.2132	0.2126	0.22	0.224	0.23	RANDOM	44.581

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.01	0.01	-0.01	-0.01	-0.01	0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.091
r_dihedral_angle_1_deg	8.092
r_dihedral_angle_2_deg	6.672
r_angle_refined_deg	0.868
r_angle_other_deg	0.604
r_chiral_restr	0.041
r_bond_other_d	0.026
r_gen_planes_refined	0.01
r_bond_refined_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19896
Nucleic Acid Atoms
Solvent Atoms	449
Heterogen Atoms	480

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.